Exploring the complexity of ecological networks using SVD entropy

class: center, middle, inverse, title-slide

# Exploring the complexity of ecological networks using SVD entropy
### Tanya Strydom, Gullio V. Dalla Riva & Timothée Poisot
### <table style="border-style:none; padding: 0 0 50px 0; background-color:transparent" class="table">
<tr>
<th style="padding:0 30px">
<a href="https://twitter.com/tanyas_08"></a>
</th>
<th style="padding:0 30px">
<a href="https://github.com/tanyas08"> </a>
</th>
</tr>
<tr style="background-color:transparent">
<th style="padding:0 30px">
<a href="https://twitter.com/tanyas_08"> @TanyaS_08 </a>
</th>
<th style="padding:0 30px">
<a href="https://github.com/tanyas08"> @TanyaS08 </a>
</th>
</tr>
</table>

---

class: center, middle

Presentation created using **{xaringan}** (the **robot** theme)

Slides available at [https://tanyas08.github.io/Talks/2020_Dec_TUKS/index.html#1](https://tanyas08.github.io/Talks/2020_Dec_TUKS/index.html#1)

---

# The Backstory

.center[species interaction networks 🕸 + fancy maths 🧮 | FAIR & Open Science ⚖️ | part-time doodler 🎨 | warm beverage fan ☕]

--
.center[
 
Participant of the 5th [Plant Functional Traits Course](https://plantfunctionaltraitscourses.w.uib.no/)

Placed a lot of focus on doing reproducible science

Inspired [this](https://doi.org/10.1002/ece3.7009) manuscript on how we can incorporate

teaching FAIR and Open Science in 
student training
]

<img src="data:image/png;base64,#img/NextGen.png" width="85%" />
 
--

---

# What is Open Science?

.center[*A global movement to promote integrity, repeatability, and transparency across all aspects of scientific research*]

.pull-left[
**Which includes:**

- Open access to publications

- Open access to data

- Open source code and data handling
]

---

# Make your Science FAIR

.center[***F**indable, **A**ccessible, **I**nteroperable and **R**eproducible*]

---

# Where to Start Though?

.footnote[[*] Respecting data sharing restrictions and embargoes]

.left-column[data lifecycle.png]

.right-column[
- Think about how you enter your data
  * Follow data and metadata standards (e.g. [DarwinCore](https://www.tdwg.org/))
  * Document it (e.g. README file) think of this as an extensive methods section

- Document data processing and analysis
 * Use code-based workflows
 * Annotate said code
 
 
- Archive data in an accessible way
 * Make as open and findable as possible* e.g. a data statement and link to archive/repository
 * Use non-propriety file formats e.g. .csv/.txt
 * Include **all** documentation
 
 
- Do some of your own research
]

---
class: inverse, middle, center

background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg)
background-position: bottom
background-size: 20%

# 1. Scripting changes

---
background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg)
background-position: bottom right
background-size: 20%

# Keep it Scripted

Ultimately after inputting your data into a file* it should remain untouched and unchanged.

.footnote[[*] Ideally using a non propriety format such as .csv or .txt]

**What does that even mean?**

- We want to keep `data_raw.csv` intact and end up with `data_clean.csv` on the other side

**Why should I script it?**
--

1. It allows you (and others) to keep track of what you changed

1. Document why you made the changes you did (*sensu lato* a lab book)

1. Avoid the all to common `_cleaned`, `_cleaned2` issue

---
class: inverse, middle, center

background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg)
background-position: bottom
background-size: 20%

# 2. Annotating code

---

# Annotations save lives (and time)

Annotating your code by adding comments makes it easier for you (and others) to understand what or why you decided to do what you did

.pull-left[
- Pseudocode can double up as annotations
  * Pseudocoding is a way of writing out your code in 'plain language' before you start coding it up
  
  
- Detail specific changes or reasoning
  * Especially when cleaning or transforming data
  ]

---
class: inverse, middle, center

background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg)
background-position: bottom
background-size: 20%

# 3. Data Archiving (with bonus version control)

---

# Get with GitHub

Think of GitHub as a google drive of sorts that you would keep your projects in - the only difference is that it has some bonus features.

* **It's Open Access:** Like a social media profile that people can click on and explore it *i.e.* you can share and showcase your work/packages/projects*.
 + This is where your data/analyses can 'live' until needed.

* **It has Version Control:** This means that every time you re-upload a file the older versions are saved (and can be recouped if needed).
  + You can do this [straight from RStudio](https://happygitwithr.com/rstudio-git-github.html)
  + This also facilitates collaboration in a big way (no more email chain!)

* **It's Designed for Programming:** Aside form simple storage of files you can design [workflows](https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions) that run jobs depending on what happens in the repository.

.footnote[[*] I find this also 'forces' me to make sure my code is readable/shareable]

---

# A GitHub 'Primer'

1. GitHub is the 'norm' in the world of Open Source  - so if you want to go open  go with GitHub

1. [Happy Git and GitHub for the useR](https://happygitwithr.com) is a great starting point if you're interested
  + especially for installing Git on your device (it can be a bit confusing)

1. You can also have private repositories
  * So you can keep your work 'hidden' but still cash in on version control and easier collaborating
  
1. As university students you qualify for a [free pro account](https://education.github.com/pack) - *go for it it*

---

# Other Ways to Open your Science